[2024-01-25 18:52:20,717] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:20,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:20,719] [INFO] DQC Reference Directory: /var/lib/cwl/stg86371cb2-cb1b-46c6-9546-c5247b4ea45e/dqc_reference
[2024-01-25 18:52:21,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:21,835] [INFO] Task started: Prodigal
[2024-01-25 18:52:21,835] [INFO] Running command: gunzip -c /var/lib/cwl/stgce16387b-63bb-4587-a4ac-69dbf0849d28/GCF_001007935.1_ASM100793v1_genomic.fna.gz | prodigal -d GCF_001007935.1_ASM100793v1_genomic.fna/cds.fna -a GCF_001007935.1_ASM100793v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:32,132] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:32,132] [INFO] Task started: HMMsearch
[2024-01-25 18:52:32,132] [INFO] Running command: hmmsearch --tblout GCF_001007935.1_ASM100793v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86371cb2-cb1b-46c6-9546-c5247b4ea45e/dqc_reference/reference_markers.hmm GCF_001007935.1_ASM100793v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:32,347] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:32,348] [INFO] Found 6/6 markers.
[2024-01-25 18:52:32,379] [INFO] Query marker FASTA was written to GCF_001007935.1_ASM100793v1_genomic.fna/markers.fasta
[2024-01-25 18:52:32,379] [INFO] Task started: Blastn
[2024-01-25 18:52:32,379] [INFO] Running command: blastn -query GCF_001007935.1_ASM100793v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86371cb2-cb1b-46c6-9546-c5247b4ea45e/dqc_reference/reference_markers.fasta -out GCF_001007935.1_ASM100793v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:32,974] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:32,977] [INFO] Selected 19 target genomes.
[2024-01-25 18:52:32,977] [INFO] Target genome list was writen to GCF_001007935.1_ASM100793v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:32,984] [INFO] Task started: fastANI
[2024-01-25 18:52:32,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgce16387b-63bb-4587-a4ac-69dbf0849d28/GCF_001007935.1_ASM100793v1_genomic.fna.gz --refList GCF_001007935.1_ASM100793v1_genomic.fna/target_genomes.txt --output GCF_001007935.1_ASM100793v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:45,354] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:45,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86371cb2-cb1b-46c6-9546-c5247b4ea45e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:45,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86371cb2-cb1b-46c6-9546-c5247b4ea45e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:45,360] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:52:45,361] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:45,361] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Nitrosomonas communis	strain=Nm2	GCA_001007935.1	44574	44574	type	True	100.0	1351	1355	95	conclusive
Nitrosomonas communis	strain=Nm2	GCA_008124795.1	44574	44574	type	True	99.8557	1191	1355	95	conclusive
Nitrosomonas nitrosa	strain=Nm90	GCA_003051105.1	52442	52442	type	True	77.6301	224	1355	95	below_threshold
Nitrosomonas supralitoralis	strain=APG5	GCA_003011925.2	2116706	2116706	type	True	77.2866	67	1355	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_900105875.1	44577	44577	type	True	77.1941	72	1355	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_001455205.1	44577	44577	type	True	77.1924	80	1355	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:45,363] [INFO] DFAST Taxonomy check result was written to GCF_001007935.1_ASM100793v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:45,364] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:45,364] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:45,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86371cb2-cb1b-46c6-9546-c5247b4ea45e/dqc_reference/checkm_data
[2024-01-25 18:52:45,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:45,405] [INFO] Task started: CheckM
[2024-01-25 18:52:45,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001007935.1_ASM100793v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001007935.1_ASM100793v1_genomic.fna/checkm_input GCF_001007935.1_ASM100793v1_genomic.fna/checkm_result
[2024-01-25 18:53:19,240] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:19,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:19,274] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:19,274] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:19,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001007935.1_ASM100793v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:19,275] [INFO] Task started: Blastn
[2024-01-25 18:53:19,275] [INFO] Running command: blastn -query GCF_001007935.1_ASM100793v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86371cb2-cb1b-46c6-9546-c5247b4ea45e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001007935.1_ASM100793v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:20,276] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:20,281] [INFO] Selected 8 target genomes.
[2024-01-25 18:53:20,282] [INFO] Target genome list was writen to GCF_001007935.1_ASM100793v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:20,300] [INFO] Task started: fastANI
[2024-01-25 18:53:20,301] [INFO] Running command: fastANI --query /var/lib/cwl/stgce16387b-63bb-4587-a4ac-69dbf0849d28/GCF_001007935.1_ASM100793v1_genomic.fna.gz --refList GCF_001007935.1_ASM100793v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001007935.1_ASM100793v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:29,717] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:29,723] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:53:29,724] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_001007935.1	s__Nitrosomonas communis	100.0	1352	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	98.46	96.92	0.96	0.92	3	conclusive
GCF_900113925.1	s__Nitrosomonas sp900113925	94.7063	1022	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114745.1	s__Nitrosomonas communis_A	90.5959	1006	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107265.1	s__Nitrosomonas sp900107265	84.7501	754	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100485.1	s__Nitrosomonas sp900100485	79.9972	567	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	97.39	97.39	0.88	0.88	2	-
GCA_016708955.1	s__Nitrosomonas sp016708955	77.2232	69	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000219585.1	s__Nitrosomonas sp000219585	76.6234	82	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:29,725] [INFO] GTDB search result was written to GCF_001007935.1_ASM100793v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:29,725] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:29,729] [INFO] DFAST_QC result json was written to GCF_001007935.1_ASM100793v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:29,729] [INFO] DFAST_QC completed!
[2024-01-25 18:53:29,729] [INFO] Total running time: 0h1m9s